Equestria Girls 3 Revenge of Mewtwo
by Lord Ashwood the 42nd
Summary: The Schools of Canerlot high and Crystal Prep were selected to go to Japan and the Pokemon regions to compete in a international Friendship Games. But the powerful Mewtwo will enact his revenge on the world from behind the scenes. Will Sunset and her friends be able to stop him or will the clone Pokemon destroy both their world and Equestria? Plus how does SciTwi fit into this?
1. Chapter 1

**_This is the parallel to the time we treasure in terms of when it happens also it will continue where that story left off._**

Our story begins back in Canterlot High School. Along the steps of the school; Sunset and her friend Derpy were reading up on news that the school paper had received. Derpy's Ursaring was playing with Sunset's Psyduck.

"It is with great pleasure that our school has been selected to take part of a joint Pokemon competition with two schools in Japan. This would be a great opportunity for our school to learn more about Japanese culture and how Pokemon has transformed their society. The trip to Japan will be from April 10-17."

"This is going to be amazing Sunset." Derpy smiled "Plus my cousin will give us special place to stay while we are staying there."

"That's very kind of her." Sunset replied. They speculated on what the might do or see when they get there. While they were talking a hooded figure walked over to the statue. She held out a strange device and studied the portal tot he world of Equestria. She reached out and touched it; it opened for her as she stared at it in amazement. Then a beeping noise came from her pocket. She pulled out a strange necklace of sorts and gave it a curious look.

"So this is where it is." She muttered

"HEY!"

The figure turned to see Sunset and Derpy running at her. They had recalled their Pokemon but had noticed her.

"Don't mess with that you don't know what it is!" Sunset cried out hoping the person didn't get swept up into Equestria.

"Wait up!" Derpy added.

The figure panicked and went behind the statue. Derpy went along one side and sunset down the other. They surrounded the figure and came from both sides only to find she was gone.

"Huh?" Derpy said looking around.

"Where did she go?" Sunset added looking too. "That was weird."

"Do you think she knew about the portal?"

"Im not sure but it did seem like it."

"I wonder how she was though." Derpy wondered.

"Maybe she had a Pokemon and used teleport." she added.

Sunset nodded thinking that was the most logical answer. Then they noticed Sonata, Aria, Rarity and the rest of their friends coming over. They joined them and went inside the school.

Far away on an unclaimed island a massive building loomed over. The night air slowly turned the blades of the windmills. Deep inside in a strange throne room a creature cloaked in shadow reached out with his hand stretched out. In an instant the3 hooded figure appeared.

"Was your mission was successful?" it said flatly

"Yes sir. I have pin pointed the exact location of where the power source. It is coming from a high school. Just as Adagio said it might be."

"Good, has the school been selected for the so called 'friendship games'?"

"Yes they have been. They will be here in a matter of days depending on when they leave and arrive here.."

"Very good. Continue with your research on this magic and see what you can determine whether or not I can use it."

The figure removed her hood and reviled to be Twilight Sparkle as she went off to continue her research. The creature stood up and went over to a window and stared outside.

"Once they get here it will be your job to bring them here. Along with any others that might pose a threat to me."

"Yes master." A almost robotic replied came as a response.

"Then you need to get ready to leave at day break."

"Yes master." and the figure left.

The strange creature looked out into the world outside. "Soon this world with reap my hate when my plan is put into affect. Humans Pokemon and anything else that will bow down in fear for the world will know my power. The power they thought they could control." His eyes went blue as his powers increased ten fold. "And the world will know the power of Mewtwo!"

 ** _I know this is pretty short start but I will work on it more once I have my fall break in two weeks. Comment Like and follow the story and have a great da readers._**


	2. Chapter 2

A few days later, Sunset got up bright and early for today what the day of the trip to Japan. She made some muffins thanks to Derpy's recipe. Sonata and Aria who had moved in with her after losing their penthouse. Apparently they used their voice on the landlord to allow them to stay there since they came to town. But Sunset didn't mind it actually felt nice having others living with her. Like having real sisters.

"Muffins are done!" She called out. Then a blur of light blue burst from the hallway to the table; Sonata beamed waiting for food. Aria; her sister groggily came out of her room and walked slowly to her chair. Sunset laughed and handed her a cup of black coffee.

"Thanks." She muttered as she took a sip. "Coffee." She sighed in content.

Sunset handed them each a plate of eggs and bacon with a blueberry muffin. They ate in silence each of them thinking of the trip to Japan. More like what to pack for the trip. They returned to their rooms to pack.

Aria was already packed so she grabbed her bags and took them down. Sunset was also back but made sure she had everything together. Sonata on the other hand was not back. She was quickly throwing clothes into a big back and some plushy too. They grabbed their Pokeballs too and were out the door waiting for the bus.

"So have any of you ..." Started Sunset but Aria shock her head.

"No we never traveled to Japan. We came here in some where in Greece and only went westward." She groaned. Sunset and the other girls love to bug her with questions of their lives living for over a 1000 years. Sonata was bubbling with excitement.

"This is so exciting!" She beamed as the bus made its way to them. They boarded it and took their seats.

"More important question is Ash's coming with us or not." Aria asked

"He say he would come. Twilight is going to speak at our old Magic School so she said he can come for a few days." Sunset replied. They made a few more stops picking up Fluttershy and Rarity. Soon they were all at at CHS. As the students who would be going to Japan stepped off to the side to broad special buses to get to the airport. Derpy was waiting for them and waved when she saw them coming her way.

"Sunset!" She cried and hugged her best friend. She hugged back and they all sat on the ground waiting for the the bus. They talked over what they would be doing in Japan.

"So what is the one you have to do I Japan once we get there?" Derpy asked.

"Im going to eat 20 bowls of ramen!" Sonata jumped thinking of all the kinds ramen. She even drooled at the thought. Aria groaned and rubbed her forehead.

"First it was tacos now it's ramen. She is such a dolt." Sunset just sighed.

Rarity spoke next. "Well as for me I will be taking a look at their kimono shops to try some on and see how their silk products can be sold to me."

"I would like to see the Pokemon and animals that are native there." Fluttershy added. She turned to Derpy. "What about you Derpy, what will you do in Japan."

"Well, I want to see my cousin Cynthia again. Also I always wanted to try on one of those summer kimonos." Then Rainbow Dash, Applejack, and Pinkie Pie came over.

"What are you guys talking about" Rainbow Dash asked getting her bags together with the others.

"We talking about what we will be doing once we get to Japan." Fluttershy replied as she took out a pokeball and let out her Eevee and petted it.

"Oh that's easy. I want to see how fast they are at sports and gaming." RD answered.

"I want to try their apples and see how they compare to American ones." Applejack remarked.

Pinkie pie just beamed. "This will be the greatest field trip ever!"

They all got ready just then the portal opened and Ash stepped out of it.

"ASH!" All the girls cheered ad hugged him. Sunset and Sonata hugged him the longest. But then another man step out from the portal too. He was tall and very odd; his smile seemed to bring unease towards Aria, Sonata, and Sunset. He snapped his fingers while Ash groaned as the man stood next to him patting his shoulder.

"Well these must be the counterparts you mentioned." He smiled poking Ash's cheek.

Ash had a irritated look. "Look I agreed to bring you with me. But if you think I will stand one minute of your nonsense I will you cast you back to Equestria."

"Ash I'm shocked. Your not going to introduce me to your friends?" he smiled.

Ash sighed "Alright, this is my friend Discord."

"Im your uncle for the day Ash." he remarked.

Sonata, Aria, and Sunset paled. "You..you..you mean Discord...Lord of Chaos and Disharmony!" They cried out in fear.

"Yes ladies that's me. But I'm a reformed just like you; sirens." Discord smirked.

"But I can read your minds, and some of you are very perverted."

Ash's wide and elbowed Discord hard and scowled at him. Discord knew he could not read minds but the thought was now in their minds and hoped he would find who would creak first. Aria blushed and tried very hard to look inconspicuous. Also the other girls glared at the man. Ash was thinking of turning Discord to stone And leaving him here until he returned.

"Oh Ash." He snapped his fingers and he was in a red and black robes and a weird crown on his head. "I am still the lord of chaos. I'm meant to have a little fun now and then."

"Great...he still has his powers in this world." Ash held his face in his hand.

They all shuddered in fear as Discord contained to smirk. Ash groaned in frustration and rubbed his head. Then they noticed how quiet it had gotten. No dabbling of students no teachers align roll call no rumbling of the buses. They all looked out to see that there was no one left there.

"Did we..." Muttered Sunset her face going blue with dread.

"Miss the Bus." added Rarity with a very pale face.

"And our class..." Derpy added next with tears in her eyes.

"TRIP TO JAPAN!" Everyone cried out in tears as most fell to the ground. Ash felt very upset for everyone as he knelt down beside a crying Fluttershy. But Discord stepped forward to the street and stretched.

"Don't worry everyone." He smiled with cheek and deviousness.

"I got this."

In another part of town a older woman sat at her desk as head mistress of the elite school Crystal Prep. A knock came to her door.

"Yes." She said with a groan. A younger and infinity more beautiful woman stepped into her office. "What is it Dean Cadense?"

Cadense gave a forced smile. "Miss Twilight Sparkle has returned from Tokyo. She is waiting outside to speak with you."

Dean Cinch smiled and stood up. 'My priced protege. What marvel are you working on now?'

"Every well. Send her in."


	3. Chapter 3

Cadense turned back and opened the door and let Twilight in. She was in her school uniform and had her hair tied up into a high bun. She seemed very tired and looked like she hasn't slept well for the last couple of nights.

"Ms. Sparkle welcome back." Headmistress Cinch smiled "I know your time in

Japan was a productive one I assume?"

Dean Cadense frowned as she left hearing that. 'Why must she work that poor girl to death. Yes she's a genius but she's still young she need friends' she thought as she left the room.

Twilight took a seat in front of the headmistress' desk. She had bags under her eyes and she seemed to be running on fumes. Her head seemed to bob almost ready to drop right there.

"MISS SPARKLE!"

"AAAAAHHHHHH!" Twilight snapped to attention and looked around. She panted then looked up at her headmistress.

"Yes I'm here I so sorry but what are we taking about." She laughed in a panic.

Ms. Cinch have a look of displeasure. "Miss Sparkle I am surprised. you would think a non stop flight form Tokyo to Capital City Washington first class no doubt would be a good time."

"Sorry miss Cinch but I don't do well on planes and sleeping on them yea can't. And I haven't slept in three days." She chuckled getting no sympathy form her principle.

She rubbed the back of her head "So not interested in that. So 'ahem' I am almost down with the finished with the 'SPIRE' it will be ready in a few more days."

At this Miss Cinch actually smiled. "That's good to hear. I was getting worried that you might not make the deadline. Especially since I got a call from the one our sponsors."

Twilight gave a confused look. "Huh.."

"They called me and informed me that they are withdrawing their funds for this school. They say they can't keep send us money if we don't know what they are investing their money into." She turns to the window and glares outside.

"They also explained to me that they will be going to our biggest rival school. Canterlot High school; a public school no less. They have been getting more attention this past year. Their been getting more attention from potential sponsorship. Their grades have improved, sporting events have increased and their enrollment has nearly doubled. I will not this school go down to a public school. Because if we loose that funding we are going to make cuts and that personal lab of your in on the top of my list." She turned back sharply making Twilight stiffen.

"That machine must be up and running when we arrive in Tokyo do I make myself clear."

Twilight just nodded and felt the sweat trickled down her back. "It will be ma'am."

"Good now get going and get ready to return to Japan."

"Wait what"

"You will be doing the demonstration of the machine are you not."

"Yes but I thought I see may family before I went back and isn't this something we could have.. Done over..." She trailed of as her headmistress glared at her.

"I like to do things in person. Now if that machine of your works and gets us more sponsors and even sell your invention. I will ensure that you will get all the funding and privacy you wish for. I dont believe it won't work it just as to work when we get there."

Twilight sighed "I will work that I will promise."

"Very good. You can return home and get some well deserved sleep. We will be departing tomorrow for the airport."

"I understand." Twilight said and got up from her chair. She turned to leave but she glanced back at the headmistress who had turned back to the window. She frowned and left. Miss Cinch smiled to herself. "I would have one of the most brilliant student in history, and my legacy as the greatest headmaster of this school will be solidified." She chuckled to herself.

Back at CHS,

"YOU HAD SOMETHING TO DO WITH THIS DIDNT YOU!" Ash yelled out shaking Discord aggressively. Rarity, Fluttershy, and Pinkie Pie were still crying Applejack was trying to call the principles but weren't getting any response. Rainbow Dash Derpy, and Sunset were holding Aria and Sonata back from joining Ash in strangling Discord.

"I'll kill him! I swear I will KILL HIM!" Aria swore tiring to get out of Rainbow Dash and Sunset's grip.

"I might have but shaking me won't get you to Japan." He sighed as Ash tried to make him see sense.

"I did I say I got this."

He got Ash off of him and cracked his fingers and rubbed his hand together. He then put one hand up and snapped his fingers.

There standing before them was a British Railway A3 Steam engine with two coaches attached to it. Everyone was staring in disbelief.

"What the hell..." RD started but Ash was now strangling the lord of chaos who's was finding this very hard to breathe with.

"Are you out of you mind!" Ash cried out. "One this is a locomotive on the damn street with no tracks. Two Japan is an island over 10,00 miles away with no bridges going into the country from Asia. AND THREE WHY A STEAM ENGINE!"

Discord snapped his fingers and dusted himself off. "Ash its as if you forgot who I am. I am the lord of chaos do you really think I couldn't make it possible for this locomotive to run on the road and water with a snap of my fingers."

Ash groaned as he slowly let out his anger. This was going to be a long trip. Sonata and Derpy were in the train cab will the others go their stuff on board the train.

Rarity loved the old English decor. Applejack felt uneasy being on a train and Rainbow Dash was still confused on how Aria knew this Discord. Pinkie Pie dawned on a Guards out fit.

"ALL ABOARD!" She Cried out waving a green Flag.

Sonata Discord and Depry played with the controls and the train started to move large clouds of steam and smoke billowed into the air. With a loud whistle the train left the high school. As the rolled alone a hooded figure gazed at the train as moved alone define all matter of logic.

'This maybe a problem for us.' It thought as its eyes glowed with power and physic energy.


	4. Chapter 4

Everyone on the train seemed a little uncomfortable except for Pinkie Pie and Sonata were enjoying themselves and Ash's is rather annoyed then being nervous. Hovering above them were dozens of tea cups and saucers each of them getting filled up by a floating teapot filled with hot chocolate. Discord walking around where in a conductor's uniform asking for tickets and Ash finally had enough. He stands up and glares.

"what on Earth are you doing?!" Ash snarled.

He was furious at Discord for bringing magic with him and exploiting themselves as they travel the crossed the land in a steam engine without any tracks. Now most of the girls are still uncomfortable usually they are just used to their magic whenever they call me up during music concerts. All except Sonata and Pinkie Pie decide to have some fun and run around the train cars exploring every bit of it.

"This is amazing!" Sonata beamed as she drank more hot chocolate.

"Chocolate!" Pinkie screamed and followed her besty.

Discord smiled as Ash held his shirt. "Relax princy boy. There is no trouble." he snapped his figures and teleported to the front of the engine. Ash looked and was impressed. The whole train was invisible. Ash sighed as the two returned to the coach and Ash sat down rubbing his head.

Meanwhile Rarity turned to Sunset "So, Who exactly is Discord" she asked. Aria and Sunset look at each other with mild discomfort and then tell the story of how Discord is the spirit of Chaos and disharmony.

"Well..." Sunset began "A 1000 years ago he ruled over Equestria for a long time before Princess Celestia and Luna defeated ham in a bottle imprisoning him in stone. He has the power to twist the very fabric of reality. Some have said that he was powerful enough that no other power in our world would have power to stand up against him."

"For us as Sirens, we kept to the western coast of Eqeastria so we never encountered him but we knew to fear his power." Aria added. Ash moved over to sit beside Sunset as she smiled at him.

"Then one day he somehow escaped his stone prison and retured to cause chaos. He turned Twilight, me and our friends into the opposites of our true selves."

"What i the oppisate of your true self Ash..." Rainbow Dash asked from the other side of the aisle. Applejack sat beside her still hesitant on the floating cups.

Ash flinched at the memory. Discord leaned in "Show i show them what you were like..."

"NO NO NO!" Ash stated "Lets just say that i was not in my strongest character." Discord snickered as Ash glared at him.

"But we did defeat you in the end." Ash rebuked as Discord lost some of his smile and looked back at Ash. "Dont leave out my grand reformation it is quite entertaining."

Ash then turns to Rainbow Dash

"So.." he asked "About the Friendship Games what are those again"

she replies "Well the Friendship Games is were Canterlot High as games and competions against Crystal Prep. Sadly we never won a match against Crystal prep in Neely 5 years. But I got everyone pumped up and ready for this year particularly with Pokemon tournaments and of course of our Pony magic."

"Rainbow Dash i am suprised i never took you being the one to cheat."

"I'm thinking of using magic added to our advantage. Isn't that what are there to do demonstrate our strenghts and abilities." Rainbow Dash tries to convince him but no avail.

"Do you even know how to even control our magic and what purpose does magic have excatly. Even if you could use it there are people out there who would try to take it from you.

Which Rainbow Dash cannot answer then Discord is very intrigued on the fact that human girls have magic.

"So these girls have magic and can use it in a non magical world." he looks over all the girls. He detects though Aria and Sonata are Sirens from Equestria and that Sunset Shimmer was also from Equeastria.

"Well well well, I never expected that this is where you ended up here." he smiled deviously as Aria and Sonata felt very small and very much afraid of the master of chaos. He turned to Sunset. "I remember you." he walked up to her as she felt very uncomfortable. "You would complian bitterly over oh Celestia would hold you back not taking your skill and powers seriously. i wanted to break my ears off all the whining you would do." she felt very selfconscious of her past mistakes but she felt Ash wrap an arm around her and gave Discord a glare who flinched at the power of it and decided to move on. Now as the train hits water it then starts running on top of the water without actually hitting it. Soon night falls everyone went to sleep. Except Ash, he was thinking particularly about the girls having more Magic and sunset talking to him about it.

"Are you thinking about our magic" she asked as he staried out into the star filled sky.

" I don't know exactly what's going on but there's something special about you girls here more than just being counterparts to Equestria. Magic just seems to resonate with you all here in this world." Sunset and Ash sit there for a moment in a slight awkward silence.

"Hehe this world. I lived in Equestria for so long i don't even call this place my homeworld anymore." he rubbed his forehead.

"I know the feeling." Sunset added. The memories of the last time they met kindled up in their minds, particularly the kiss they shared. Both were quiet for some time.

"Thank you" Ash smiled at her as they looked at each other. "I didnt thank you properly for saving me from the mind control."

"It's no big deal but I still thinks about it." Ash moves closer to her and pulls her into a side hug letting her rest her head on his shoulders.

"Do you still have those feelings Sunset, do you still love me" He could feel her face heat up with embarrassment but her only reply was nodding her head. Ash holds her a little tighter trying to give her some reassurance and comfort.

Sunset finally reply. "I know that I could never be yours Ash. I know you love Twilight dearly and im happy for the two of you but." she clinched his arm as tears pooled in her eyes. "But I cant seem to move on. I still love you Ash and i dont know how to move pass this."

This saddened him hearing her broken heart but knew; as long as he's married to Twilight and his heart belongs to her there can't be a real future between them as much as she once wanted one to be. He never had deep feelings for her; he did respect and cared for her and wanted her to be happy but the way he saw her as his younger sister. She started to cry holding Ash and he just lets her cry keeping a nice tight hold on her just give some sort of reassurance. He feels terrible for her and wants to help her butt there's nothing he can really do but they continue being her friend

"I admit..." she sniffled looking at him "if this is all that we could be, I am still lucky to be your friend."

"Sunset Shimmer." he muttered whiping her tears away. "You mean more to me than just my friend and aura student. I know you have a great destiny ahead. I dont know how to help you with your feelings, but I want you to know that I am here for you no matter what. I will care about you for a long as i live but as my sister. And I know you can move on and I know you will find joy." She smiles and he lets her hold his arm as she let sleep take over her. Ash smiled as she slept thinking on what he said. 'Me an older brother, i might have to make that a reality.'

Neither one of them seemed a pair of wacky eyes staring in on them.


End file.
